Vineet Bafna

The paper improves genome annotation for Chinese hamster by integrating RNA-Seq, proteomics, and Ribo-Seq, identifying new proteins and translational events, and addressing retroviral contamination in CHO cell lines.

The paper develops methods to compute statistical significance of interval overlaps and introduces a tool, iStat, to analyze simulated and real datasets.

adVNTR is a method for genotyping Variable Number Tandem Repeats using Hidden Markov Models, applicable to short-read and single molecule sequencing data.

AmpliconArchitect reconstructs focal amplifications in cancer genomes, revealing novel insights into extrachromosomal mechanisms and oncoviral pathogenesis.

This paper introduces a method for accurate single-cell genome sequencing and haplotyping with low error rates and long haplotype assembly.

The paper introduces AbScan, a proteogenomic method to identify antibody peptides from RNA-seq data, and applies it to colorectal cancer samples to find correlations between antibody peptides and survival.